From 41e207d762c067ec55bcc40922a66aaf2ef977a0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 12 Jan 2010 17:16:57 +0000 Subject: [PATCH 1/7] Added comments. --- Cantera/src/kinetics/InterfaceKinetics.h | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 3de46a1f1..08cc525e0 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -629,6 +629,15 @@ namespace Cantera { //! boolean indicating whether mechanism has been finalized bool m_finalized; bool m_has_coverage_dependence; + + //! Boolean flag indicating whether any reaction in the mechanism + //! has a beta electrochemical parameter. + /*! + * If this is true, the the Butler-Volmer correction is applied + * to the forward reaction rate for those reactions. + * + * fac = exp ( - beta * (delta_phi)) + */ bool m_has_electrochem_rxns; int m_ioFlag; From 3d392242d966a68f634abd02655ba5501af350ca Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 12 Jan 2010 21:23:08 +0000 Subject: [PATCH 2/7] Added documentation for an external int --- Cantera/src/equil/MultiPhase.h | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Cantera/src/equil/MultiPhase.h b/Cantera/src/equil/MultiPhase.h index fa96148c3..516dfbc31 100644 --- a/Cantera/src/equil/MultiPhase.h +++ b/Cantera/src/equil/MultiPhase.h @@ -825,6 +825,11 @@ namespace Cantera { vector_int & orderVectorElements); #ifdef DEBUG_MODE + //! External int that is used to turn on debug printing for the + //! BasisOptimze program. + /*! + * Set this to 1 if you want debug printing from BasisOptimize. + */ extern int BasisOptimize_print_lvl; #endif } From ab38d29228a9255b1cd8b23ac0c71b12516dac1e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 12 Jan 2010 21:27:32 +0000 Subject: [PATCH 3/7] Fixed a doxygen compatibility problem. --- Cantera/src/base/ctml.cpp | 7 ++++--- Cantera/src/base/ctml.h | 4 ++-- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index 640cfa5dd..8de42e90f 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -878,7 +878,7 @@ namespace ctml { * @param v Output vector of floats containing the floatArray information. * @param convert Conversion to SI is carried out if this boolean is * True. The default is true. - * @param typeString String name of the type attribute. This is an optional + * @param unitsString String name of the type attribute. This is an optional * parameter. The default is to have an empty string. * The only string that is recognized is actEnergy. * Anything else has no effect. This affects what @@ -888,8 +888,9 @@ namespace ctml { * * @return Returns the number of floats read */ - int getFloatArray(const Cantera::XML_Node& node, vector_fp& v, const bool convert, - const std::string unitsString, const std::string nodeName) { + int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp& v, + const bool convert, const std::string unitsString, + const std::string nodeName) { string::size_type icom; string numstr; doublereal dtmp; diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 2fe84d95b..85d6f8a3b 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -358,7 +358,7 @@ namespace ctml { * @param v Output vector of floats containing the floatArray information. * @param convert Conversion to SI is carried out if this boolean is * True. The default is true. - * @param typeString String name of the type attribute. This is an optional + * @param unitsString String name of the type attribute. This is an optional * parameter. The default is to have an empty string. * The only string that is recognized is actEnergy. * Anything else has no effect. This affects what @@ -368,7 +368,7 @@ namespace ctml { * @return Returns the number of floats read into v. */ int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp& v, - const bool convert=true, const std::string typeString="", + const bool convert=true, const std::string unitsString="", const std::string nodeName = "floatArray"); //! This function interprets the value portion of an XML element From bedb3145452d5c3f77cf36986cde1555274edd6d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 12 Jan 2010 21:34:40 +0000 Subject: [PATCH 4/7] Eliminated a doxygen error. --- Cantera/src/base/misc.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Cantera/src/base/misc.cpp b/Cantera/src/base/misc.cpp index 30d8d9a90..b8893514e 100644 --- a/Cantera/src/base/misc.cpp +++ b/Cantera/src/base/misc.cpp @@ -439,6 +439,8 @@ namespace Cantera { //! Typedef for map between a thread and the message typedef std::map< cthreadId_t, pMessages_t > threadMsgMap_t ; + //! Class that stores thread messages for each thread, and retrieves them + //! based on the thread id. class ThreadMessages { public: From 8ea0c8197e143436b4754ef65e3748d0159c1219 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 13 Jan 2010 22:12:27 +0000 Subject: [PATCH 5/7] Made sure all double values were doublereal --- Cantera/src/kinetics/GRI_30_Kinetics.cpp | 10 +- Cantera/src/kinetics/GRI_30_Kinetics.h | 8 +- Cantera/src/kinetics/GasKineticsWriter.h | 14 +-- Cantera/src/kinetics/ImplicitChem.cpp | 2 +- Cantera/src/kinetics/ImplicitSurfChem.cpp | 16 +-- Cantera/src/kinetics/ImplicitSurfChem.h | 16 +-- Cantera/src/kinetics/InterfaceKinetics.cpp | 2 +- Cantera/src/kinetics/InterfaceKinetics.h | 9 +- Cantera/src/kinetics/ReactionPath.cpp | 8 +- Cantera/src/kinetics/ReactionPath.h | 15 +-- Cantera/src/kinetics/RxnRates.h | 2 +- Cantera/src/kinetics/importKinetics.cpp | 14 +-- Cantera/src/kinetics/solveSP.cpp | 140 ++++++++++----------- Cantera/src/kinetics/solveSP.h | 80 ++++++------ 14 files changed, 170 insertions(+), 166 deletions(-) diff --git a/Cantera/src/kinetics/GRI_30_Kinetics.cpp b/Cantera/src/kinetics/GRI_30_Kinetics.cpp index dd01e524d..1d5a1ba85 100644 --- a/Cantera/src/kinetics/GRI_30_Kinetics.cpp +++ b/Cantera/src/kinetics/GRI_30_Kinetics.cpp @@ -85,8 +85,8 @@ namespace Cantera { } - void GRI_30_Kinetics::update_rates(double t, double tlog, double* rf) { - double rt = 1.0/t; + void GRI_30_Kinetics::update_rates(doublereal t, doublereal tlog, doublereal * rf) { + doublereal rt = 1.0/t; rf[0] = exp(25.5108 + -1 * tlog); rf[1] = exp(26.9379 + -1 * tlog); rf[2] = exp(3.65584 + 2.7 * tlog - 3150.48 * rt); @@ -291,7 +291,7 @@ namespace Cantera { } - void GRI_30_Kinetics::update_kc(const double* a, double exp_c0, double* rkc) { + void GRI_30_Kinetics::update_kc(const doublereal * a, doublereal exp_c0, doublereal * rkc) { rkc[0] = a[3]*exp_c0/(a[2]*a[2]); rkc[1] = a[4]*exp_c0/(a[1]*a[2]); rkc[2] = a[1]*a[4]/(a[0]*a[2]); @@ -604,7 +604,7 @@ namespace Cantera { } - void GRI_30_Kinetics::get_wdot(const double* rop, double* wdot) { + void GRI_30_Kinetics::get_wdot(const doublereal * rop, doublereal * wdot) { wdot[0] = - rop[2] + rop[7] + rop[38] + rop[39] + rop[40] + rop[41] + rop[44] + rop[46] + rop[48] + rop[50] + rop[52] + rop[54] + rop[57] + rop[59] + rop[64] + rop[67] + rop[68] + rop[72] + rop[74] + rop[76] + rop[77] + rop[79] - rop[82] - rop[83] - rop[125] - rop[135] + rop[136] - rop[145] - rop[171] + rop[173] + rop[190] + rop[196] + rop[201] + rop[208] + rop[213] - rop[220] + rop[265] + rop[275] + rop[276] + rop[283] + rop[287] - rop[288] + rop[292] + rop[298] + rop[299] + rop[308] + rop[313]; wdot[1] = - rop[1] + rop[2] + rop[5] + rop[6] + rop[8] + rop[9] + rop[13] + rop[20] + rop[23] + rop[27] - rop[32] - rop[33] - rop[34] - rop[35] - rop[36] - rop[37] - 2*rop[38] - 2*rop[39] - 2*rop[40] - 2*rop[41] - rop[42] - rop[43] - rop[44] - rop[45] - rop[46] - rop[47] - rop[48] - rop[49] - rop[50] - rop[51] - rop[52] - rop[53] - rop[54] - rop[55] - rop[56] - rop[57] - rop[58] - rop[59] - rop[60] - rop[61] - rop[62] - rop[64] - rop[65] - rop[66] - rop[67] - rop[68] - rop[69] - rop[70] - rop[71] - rop[72] - rop[73] - rop[74] - rop[75] - rop[76] - rop[77] - rop[78] - rop[79] - rop[80] + rop[83] + rop[89] + rop[90] + rop[91] + rop[93] + rop[98] + rop[105] + rop[106] + rop[107] + rop[122] + rop[123] + rop[125] + rop[126] + rop[127] + rop[128] + rop[129] + rop[132] + rop[134] + rop[135] + rop[137] + rop[143] + rop[145] + rop[148] + rop[158] + rop[165] + rop[166] + rop[171] + rop[179] - rop[182] - rop[188] + rop[189] - rop[190] + rop[191] + rop[195] + rop[198] + rop[200] - rop[201] + rop[203] + rop[204] - rop[208] - rop[211] - rop[213] + rop[217] + rop[220] - rop[222] + rop[223] + rop[229] + rop[230] + rop[233] + rop[234] - rop[236] + rop[246] + rop[248] + rop[250] + rop[251] + rop[253] + rop[256] + rop[259] - rop[260] - rop[264] - rop[265] - rop[270] - rop[271] + rop[274] - rop[276] + rop[283] + rop[284] + rop[285] + 2*rop[289] + 2*rop[291] - rop[298] - rop[299] - rop[303] + rop[304] - rop[307] - rop[308] - rop[313] - rop[319] - rop[320]; wdot[2] = - 2*rop[0] - rop[1] - rop[2] - rop[3] - rop[4] - rop[5] - rop[6] - rop[7] - rop[8] - rop[9] - rop[10] - rop[11] - rop[12] - rop[13] - rop[14] - rop[15] - rop[16] - rop[17] - rop[18] - rop[19] - rop[20] - rop[21] - rop[22] - rop[23] - rop[24] - rop[25] - rop[26] - rop[27] - rop[28] - rop[29] + rop[30] + rop[37] + rop[43] + rop[85] + rop[121] + rop[124] + rop[154] + rop[177] + rop[178] - rop[180] - rop[181] + rop[184] - rop[186] - rop[187] - rop[189] + rop[193] - rop[199] - rop[200] - rop[206] - rop[207] - rop[212] - rop[216] + rop[219] - rop[221] - rop[230] - rop[231] - rop[232] + rop[243] + rop[245] - rop[256] - rop[257] + rop[258] - rop[261] - rop[262] - rop[263] - rop[278] - rop[283] - rop[284] - rop[285] + rop[290] + rop[293] - rop[295] - rop[296] - rop[304] - rop[312] - rop[318]; @@ -661,7 +661,7 @@ namespace Cantera { } - void GRI_30_Kinetics::eval_ropnet(const double* c, const double* rf, const double* rkc, double* r) { + void GRI_30_Kinetics::eval_ropnet(const doublereal * c, const doublereal * rf, const doublereal * rkc, doublereal * r) { r[0] = rf[0] * (c[2] * c[2] - rkc[0] * c[3]); r[1] = rf[1] * (c[2] * c[1] - rkc[1] * c[4]); r[2] = rf[2] * (c[2] * c[0] - rkc[2] * c[1] * c[4]); diff --git a/Cantera/src/kinetics/GRI_30_Kinetics.h b/Cantera/src/kinetics/GRI_30_Kinetics.h index 094c61289..98494f1f2 100644 --- a/Cantera/src/kinetics/GRI_30_Kinetics.h +++ b/Cantera/src/kinetics/GRI_30_Kinetics.h @@ -42,10 +42,10 @@ namespace Cantera { void gri30_update_rates_T(); void gri30_updateROP(); void gri30_updateKc(); - void get_wdot(const doublereal* rop, doublereal* wdot); - void update_kc(const double* grt, double c0, double* rkc); - void update_rates(double t, double tlog, double* rf); - void eval_ropnet(const double* c, const double* rf, const double* rkc, double* r); + void get_wdot(const doublereal * rop, doublereal * wdot); + void update_kc(const doublereal * grt, doublereal c0, doublereal * rkc); + void update_rates(doublereal t, doublereal tlog, doublereal * rf); + void eval_ropnet(const doublereal * c, const doublereal * rf, const doublereal * rkc, doublereal * r); }; } diff --git a/Cantera/src/kinetics/GasKineticsWriter.h b/Cantera/src/kinetics/GasKineticsWriter.h index 88b07a213..ccfb8486c 100644 --- a/Cantera/src/kinetics/GasKineticsWriter.h +++ b/Cantera/src/kinetics/GasKineticsWriter.h @@ -63,7 +63,7 @@ namespace Cantera { void writeGetNetProductionRates(std::ostream& s, int nsp, int nrxns) { int i, k; - s << "void get_wdot(const double* rop, double* wdot) {" << std::endl; + s << "void get_wdot(const doublereal * rop, doublereal * wdot) {" << std::endl; for (k = 0; k < nsp; k++) { s << " wdot[" << k << "] = "; doublereal net; @@ -94,8 +94,8 @@ namespace Cantera { void writeUpdateKc(std::ostream& s, int nsp, int nrxns) { int i, k, n, nn, ir; - s << "void update_kc(const double* a, " - "double exp_c0, double* rkc) {" << endl; + s << "void update_kc(const doublereal * a, " + "doublereal exp_c0, doublereal* rkc) {" << endl; for (i = 0; i != m_nrev; i++) { //if (isReversible(i)) { ir = m_revindex[i]; @@ -134,8 +134,8 @@ namespace Cantera { void writeEvalRopnet(std::ostream& s) { int i; - s << "void eval_ropnet(const double* c, " - "const double* rf, const double* rkc, double* r) {" << endl; + s << "void eval_ropnet(const doublereal* c, " + "const doublereal * rf, const doublereal * rkc, doublereal* r) {" << endl; for (i = 0; i < m_ii; i++) { s << " r[" << i << "] = rf[" << i << "] * (" << m_reactantWriter.mult(i); @@ -151,8 +151,8 @@ namespace Cantera { void writeUpdateRates(std::ostream& s) { - s << "void update_rates(double t, double tlog, double* rf) {" << endl; - s << " double rt = 1.0/t;" << endl; + s << "void update_rates(doublereal t, doublereal tlog, doublereal * rf) {" << endl; + s << " doublereal rt = 1.0/t;" << endl; m_rates.writeUpdate(s, "rf"); s << "}" << endl; } diff --git a/Cantera/src/kinetics/ImplicitChem.cpp b/Cantera/src/kinetics/ImplicitChem.cpp index 5a05e2f76..58192ffb7 100644 --- a/Cantera/src/kinetics/ImplicitChem.cpp +++ b/Cantera/src/kinetics/ImplicitChem.cpp @@ -38,7 +38,7 @@ namespace Cantera { // overloaded method of FuncEval. Called by the integrator to // get the initial conditions. - void ImplicitChem::getInitialConditions(double t0, size_t leny, double* y) + void ImplicitChem::getInitialConditions(doublereal t0, size_t leny, doublereal * y) { m_thermo->getMassFractions(y); m_h0 = m_thermo->enthalpy_mass(); diff --git a/Cantera/src/kinetics/ImplicitSurfChem.cpp b/Cantera/src/kinetics/ImplicitSurfChem.cpp index 28e82d45a..8334ae95f 100644 --- a/Cantera/src/kinetics/ImplicitSurfChem.cpp +++ b/Cantera/src/kinetics/ImplicitSurfChem.cpp @@ -132,8 +132,8 @@ namespace Cantera { // overloaded method of FuncEval. Called by the integrator to // get the initial conditions. - void ImplicitSurfChem::getInitialConditions(double t0, size_t lenc, - double* c) + void ImplicitSurfChem::getInitialConditions(doublereal t0, size_t lenc, + doublereal * c) { int loc = 0; for (int n = 0; n < m_nsurf; n++) { @@ -234,7 +234,7 @@ namespace Cantera { /* * time scale - time over which to integrate equations */ - double time_scale = timeScaleOverride; + doublereal time_scale = timeScaleOverride; /* * */ @@ -263,8 +263,8 @@ namespace Cantera { getConcSpecies(DATA_PTR(m_concSpecies)); InterfaceKinetics *ik = m_vecKinPtrs[0]; ThermoPhase &tp = ik->thermo(0); - double TKelvin = tp.temperature(); - double PGas = tp.pressure(); + doublereal TKelvin = tp.temperature(); + doublereal PGas = tp.pressure(); /* * Make sure that there is a common temperature and * pressure for all ThermoPhase objects belonging to the @@ -275,8 +275,8 @@ namespace Cantera { setCommonState_TP(TKelvin, PGas); } - double reltol = 1.0E-6; - double atol = 1.0E-20; + doublereal reltol = 1.0E-6; + doublereal atol = 1.0E-20; /* * Install a filter for negative concentrations. One of the @@ -379,7 +379,7 @@ namespace Cantera { * Pressure = Pascal */ void ImplicitSurfChem:: - setCommonState_TP(double TKelvin, double PresPa) { + setCommonState_TP(doublereal TKelvin, doublereal PresPa) { int nphases = m_nsurf; for (int ip = 0; ip < nphases; ip++) { ThermoPhase *TP_ptr = m_surf[ip]; diff --git a/Cantera/src/kinetics/ImplicitSurfChem.h b/Cantera/src/kinetics/ImplicitSurfChem.h index adc0fcdce..4074f4de5 100644 --- a/Cantera/src/kinetics/ImplicitSurfChem.h +++ b/Cantera/src/kinetics/ImplicitSurfChem.h @@ -212,7 +212,7 @@ namespace Cantera { * @param TKelvin input temperature (kelvin) * @param PresPa input pressure in pascal. */ - void setCommonState_TP(double TKelvin, double PresPa); + void setCommonState_TP(doublereal TKelvin, doublereal PresPa); //! Returns a reference to the vector of pointers to the @@ -245,25 +245,25 @@ namespace Cantera { * The lenth is equal to the sum of the number of surface * sites in all the surface phases */ - void updateState(doublereal* y); + void updateState(doublereal *y); //! vector of pointers to surface phases. - std::vector m_surf; + std::vector m_surf; //! Vector of pointers to bulk phases - std::vector m_bulkPhases; + std::vector m_bulkPhases; //! vector of pointers to InterfaceKinetics objects - std::vector m_vecKinPtrs; + std::vector m_vecKinPtrs; //! Vector of number of species in each Surface Phase - vector_int m_nsp; + vector_int m_nsp; //! index of the surface phase in each InterfaceKinetics object - vector_int m_surfindex; + vector_int m_surfindex; - vector_int m_specStartIndex; + vector_int m_specStartIndex; //! Total number of surface phases. /*! diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 98df1c8fd..090b8585e 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -425,7 +425,7 @@ namespace Cantera { */ doublereal eamod; #ifdef DEBUG_KIN_MODE - double ea; + doublereal ea; #endif int nct = m_beta.size(); int irxn; diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 08cc525e0..c1b0343a8 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -38,8 +38,9 @@ namespace Cantera { class ImplicitSurfChem; - /** - * Holds mechanism-specific data. + //! This class holds mechanism-specific data. + /*! + * */ class InterfaceKineticsData { public: @@ -47,9 +48,11 @@ namespace Cantera { m_ROP_ok(false), m_temp(0.0), m_logtemp(0.0) {} + //! Virtual destructor virtual ~InterfaceKineticsData(){} - doublereal m_logp0, m_logc0; + doublereal m_logp0; + doublereal m_logc0; array_fp m_ropf; array_fp m_ropr; array_fp m_ropnet; diff --git a/Cantera/src/kinetics/ReactionPath.cpp b/Cantera/src/kinetics/ReactionPath.cpp index af42f38a2..fc92869da 100644 --- a/Cantera/src/kinetics/ReactionPath.cpp +++ b/Cantera/src/kinetics/ReactionPath.cpp @@ -136,7 +136,7 @@ namespace Cantera { vector_int ReactionPathDiagram::reactions() { int i, npaths = nPaths(); - double flmax = 0.0, flxratio; + doublereal flmax = 0.0, flxratio; Path* p; for (i = 0; i < npaths; i++) { @@ -163,7 +163,7 @@ namespace Cantera { } void ReactionPathDiagram::add(ReactionPathDiagram& d) { -// double f1, f2; +// doublereal f1, f2; // int nnodes = nNodes(); // if (nnodes != d.nNodes()) { // throw CanteraError("ReactionPathDiagram::add", @@ -205,7 +205,7 @@ namespace Cantera { } void ReactionPathDiagram::writeData(ostream& s) { - double f1, f2; + doublereal f1, f2; int nnodes = nNodes(); int i1, i2, k1, k2; s << title << endl; @@ -275,7 +275,7 @@ namespace Cantera { int nnodes = nNodes(); int kbegin, kend, i1, i2, k1, k2; - double flx; + doublereal flx; // draw paths representing net flows if (flow_type == NetFlow) diff --git a/Cantera/src/kinetics/ReactionPath.h b/Cantera/src/kinetics/ReactionPath.h index f2ccf67d6..7cff095e7 100644 --- a/Cantera/src/kinetics/ReactionPath.h +++ b/Cantera/src/kinetics/ReactionPath.h @@ -70,15 +70,16 @@ namespace Cantera { /// add a path to or from this node void addPath(Path* path); - double outflow() {return m_out;} - double inflow() {return m_in;} - double netOutflow() {return m_out - m_in;} + doublereal outflow() {return m_out;} + doublereal inflow() {return m_in;} + doublereal netOutflow() {return m_out - m_in;} void printPaths(); protected: - double m_in, m_out; + doublereal m_in; + doublereal m_out; path_list m_paths; }; @@ -216,10 +217,10 @@ namespace Cantera { doublereal x_size, y_size; std::string name, dot_options; flow_t flow_type; - double scale; - double arrow_width; + doublereal scale; + doublereal arrow_width; bool show_details; - double arrow_hue; + doublereal arrow_hue; protected: diff --git a/Cantera/src/kinetics/RxnRates.h b/Cantera/src/kinetics/RxnRates.h index 44f0c6a70..4e3d495ad 100644 --- a/Cantera/src/kinetics/RxnRates.h +++ b/Cantera/src/kinetics/RxnRates.h @@ -321,7 +321,7 @@ namespace Cantera { } doublereal updateRC(doublereal logT, doublereal recipT) const { - double lres = update(logT, recipT); + doublereal lres = update(logT, recipT); return exp(lres); } diff --git a/Cantera/src/kinetics/importKinetics.cpp b/Cantera/src/kinetics/importKinetics.cpp index fd6b5a1c4..e40a1df84 100644 --- a/Cantera/src/kinetics/importKinetics.cpp +++ b/Cantera/src/kinetics/importKinetics.cpp @@ -96,7 +96,7 @@ namespace Cantera { void checkRxnElementBalance(Kinetics& kin, const ReactionData &rdata, doublereal errorTolerance) { int index, klocal, n, kp, kr, m, nel; - double kstoich; + doublereal kstoich; map bal, balr, balp; bal.clear(); @@ -351,8 +351,8 @@ namespace Cantera { int ispKinetics = kin.kineticsSpeciesIndex(spname); int ispPhaseIndex = kin.speciesPhaseIndex(ispKinetics); - double ispMW = th.molecularWeights()[isp]; - double sc; + doublereal ispMW = th.molecularWeights()[isp]; + doublereal sc; // loop over the reactants for (int n = 0; n < nr; n++) { @@ -760,9 +760,9 @@ namespace Cantera { int np = rdata.products.size(); for (int i = 0; i < np; i++) { int k = rdata.products[i]; - double po = rdata.porder[i]; + doublereal po = rdata.porder[i]; AssertTrace(po == rdata.pstoich[i]); - double chk = po - 1.0 * int(po); + doublereal chk = po - 1.0 * int(po); if (chk != 0.0) { /* * put in a check here that k is a single species phase. @@ -779,9 +779,9 @@ namespace Cantera { int nr = rdata.reactants.size(); for (int i = 0; i < nr; i++) { int k = rdata.reactants[i]; - double ro = rdata.rorder[i]; + doublereal ro = rdata.rorder[i]; AssertTrace(ro == rdata.rstoich[i]); - double chk = ro - 1.0 * int(ro); + doublereal chk = ro - 1.0 * int(ro); if (chk != 0.0) { /* * put in a check here that k is a single species phase. diff --git a/Cantera/src/kinetics/solveSP.cpp b/Cantera/src/kinetics/solveSP.cpp index a44757365..660e1dd05 100644 --- a/Cantera/src/kinetics/solveSP.cpp +++ b/Cantera/src/kinetics/solveSP.cpp @@ -30,17 +30,17 @@ namespace Cantera { * STATIC ROUTINES DEFINED IN THIS FILE ***************************************************************************/ - static double calc_damping(double *x, double *dx, int dim, int *); - static double calcWeightedNorm(const double [], const double dx[], int); + static doublereal calc_damping(doublereal *x, doublereal *dx, int dim, int *); + static doublereal calcWeightedNorm(const doublereal [], const doublereal dx[], int); /*************************************************************************** * LAPACK PROTOTYPES ***************************************************************************/ //#define FSUB_TYPE void // extern "C" { - // extern FSUB_TYPE dgetrf_(int *, int *, double *, int *, int [], int *); - // extern FSUB_TYPE dgetrs_(char *, int *, int *, double *, int *, int [], - // double [], int *, int *, unsigned int); + // extern FSUB_TYPE dgetrf_(int *, int *, doublereal *, int *, int [], int *); + // extern FSUB_TYPE dgetrs_(char *, int *, int *, doublereal *, int *, int [], + // doublereal [], int *, int *, unsigned int); // } /***************************************************************************** * PROTOTYPES and PREPROC DIRECTIVES FOR MISC. ROUTINES @@ -208,10 +208,10 @@ namespace Cantera { * surface species production rate = 0 and that the bulk fractions are * proportional to their production rates. */ - int solveSP::solveSurfProb(int ifunc, double time_scale, double TKelvin, - double PGas, double reltol, double abstol) + int solveSP::solveSurfProb(int ifunc, doublereal time_scale, doublereal TKelvin, + doublereal PGas, doublereal reltol, doublereal abstol) { - double EXTRA_ACCURACY = 0.001; + doublereal EXTRA_ACCURACY = 0.001; if (ifunc == SFLUX_JACOBIAN) { EXTRA_ACCURACY *= 0.001; } @@ -220,24 +220,24 @@ namespace Cantera { int label_t=-1; /* Species IDs for time control */ int label_d; /* Species IDs for damping control */ int label_t_old=-1; - double label_factor = 1.0; + doublereal label_factor = 1.0; int iter=0; // iteration number on numlinear solver int iter_max=1000; // maximum number of nonlinear iterations int nrhs=1; - double deltaT = 1.0E-10; // Delta time step - double damp=1.0, tmp; + doublereal deltaT = 1.0E-10; // Delta time step + doublereal damp=1.0, tmp; // Weighted L2 norm of the residual. Currently, this is only // used for IO purposes. It doesn't control convergence. // Therefore, it is turned off when DEBUG_SOLVESP isn't defined. - double resid_norm; - double inv_t = 0.0; - double t_real = 0.0, update_norm = 1.0E6; + doublereal resid_norm; + doublereal inv_t = 0.0; + doublereal t_real = 0.0, update_norm = 1.0E6; bool do_time = false, not_converged = true; #ifdef DEBUG_SOLVESP #ifdef DEBUG_SOLVESP_TIME - double t1; + doublereal t1; #endif #else if (m_ioflag > 1) { @@ -548,7 +548,7 @@ namespace Cantera { /* * Update the surface states of the surface phases. */ - void solveSP::updateState(const double *CSolnSP) { + void solveSP::updateState(const doublereal *CSolnSP) { int loc = 0; for (int n = 0; n < m_numSurfPhases; n++) { m_ptrsSurfPhase[n]->setConcentrations(CSolnSP + loc); @@ -565,7 +565,7 @@ namespace Cantera { /* * Update the mole fractions for phases which are part of the equation set */ - void solveSP::updateMFSolnSP(double *XMolSolnSP) { + void solveSP::updateMFSolnSP(doublereal *XMolSolnSP) { for (int isp = 0; isp < m_numSurfPhases; isp++) { int keqnStart = m_eqnIndexStartSolnPhase[isp]; m_ptrsSurfPhase[isp]->getMoleFractions(XMolSolnSP + keqnStart); @@ -582,7 +582,7 @@ namespace Cantera { * Update the mole fractions for phases which are part of a single * interfacial kinetics object */ - void solveSP::updateMFKinSpecies(double *XMolKinSpecies, int isp) { + void solveSP::updateMFKinSpecies(doublereal *XMolKinSpecies, int isp) { InterfaceKinetics *m_kin = m_objects[isp]; int nph = m_kin->nPhases(); for (int iph = 0; iph < nph; iph++) { @@ -596,11 +596,11 @@ namespace Cantera { * Update the vector that keeps track of the largest species in each * surface phase. */ - void solveSP::evalSurfLarge(const double *CSolnSP) { + void solveSP::evalSurfLarge(const doublereal *CSolnSP) { int kindexSP = 0; for (int isp = 0; isp < m_numSurfPhases; isp++) { int nsp = m_nSpeciesSurfPhase[isp]; - double Clarge = CSolnSP[kindexSP]; + doublereal Clarge = CSolnSP[kindexSP]; m_spSurfLarge[isp] = 0; kindexSP++; for (int k = 1; k < nsp; k++, kindexSP++) { @@ -622,14 +622,14 @@ namespace Cantera { * This routine uses the m_numEqn1 and m_netProductionRatesSave vectors * as temporary internal storage. */ - void solveSP::fun_eval(double* resid, const double *CSoln, - const double *CSolnOld, const bool do_time, - const double deltaT) + void solveSP::fun_eval(doublereal * resid, const doublereal *CSoln, + const doublereal *CSolnOld, const bool do_time, + const doublereal deltaT) { int isp, nsp, kstart, k, kindexSP, kins, kspecial; - double lenScale = 1.0E-9; - double sd = 0.0; - double grRate; + doublereal lenScale = 1.0E-9; + doublereal sd = 0.0; + doublereal grRate; if (m_numSurfPhases > 0) { /* * update the surface concentrations with the input surface @@ -690,7 +690,7 @@ namespace Cantera { if (m_bulkFunc == BULK_DEPOSITION) { kindexSP = m_numTotSurfSpecies; for (isp = 0; isp < m_numBulkPhasesSS; isp++) { - double *XBlk = DATA_PTR(m_numEqn1); + doublereal *XBlk = DATA_PTR(m_numEqn1); //ThermoPhase *THptr = m_bulkPhasePtrs[isp]; //THptr->getMoleFractions(XBlk); nsp = m_nSpeciesSurfPhase[isp]; @@ -743,14 +743,14 @@ namespace Cantera { * This routine uses the m_numEqn2 vector * as temporary internal storage. */ - void solveSP::resjac_eval(std::vector &JacCol, - double resid[], double CSoln[], - const double CSolnOld[], const bool do_time, - const double deltaT) + void solveSP::resjac_eval(std::vector &JacCol, + doublereal resid[], doublereal CSoln[], + const doublereal CSolnOld[], const bool do_time, + const doublereal deltaT) { int kColIndex = 0, nsp, jsp, i, kCol; - double dc, cSave, sd; - double *col_j; + doublereal dc, cSave, sd; + doublereal *col_j; /* * Calculate the residual */ @@ -798,7 +798,7 @@ namespace Cantera { #define APPROACH 0.80 - static double calc_damping(double x[], double dxneg[], int dim, int *label) + static doublereal calc_damping(doublereal x[], doublereal dxneg[], int dim, int *label) /* This function calculates a damping factor for the Newton iteration update * vector, dxneg, to insure that all site and bulk fractions, x, remain @@ -813,8 +813,8 @@ namespace Cantera { { int i; - double damp = 1.0, xnew, xtop, xbot; - static double damp_old = 1.0; + doublereal damp = 1.0, xnew, xtop, xbot; + static doublereal damp_old = 1.0; *label = -1; @@ -873,9 +873,9 @@ namespace Cantera { * This function calculates the norm of an update, dx[], * based on the weighted values of x. */ - static double calcWeightedNorm(const double wtX[], const double dx[], int dim) { - double norm = 0.0; - double tmp; + static doublereal calcWeightedNorm(const doublereal wtX[], const doublereal dx[], int dim) { + doublereal norm = 0.0; + doublereal tmp; if (dim == 0) return 0.0; for (int i = 0; i < dim; i++) { tmp = dx[i] / wtX[i]; @@ -889,12 +889,12 @@ namespace Cantera { * concentration unknowns and the residual unknowns. * */ - void solveSP::calcWeights(double wtSpecies[], double wtResid[], - const Array2D &Jac, const double CSoln[], - const double abstol, const double reltol) + void solveSP::calcWeights(doublereal wtSpecies[], doublereal wtResid[], + const Array2D &Jac, const doublereal CSoln[], + const doublereal abstol, const doublereal reltol) { int k, jcol, kindex, isp, nsp; - double sd; + doublereal sd; /* * First calculate the weighting factor for the concentrations of * the surface species and bulk species. @@ -941,13 +941,13 @@ namespace Cantera { * * Maximum time step set to time_scale. */ - double solveSP:: - calc_t(double netProdRateSolnSP[], double XMolSolnSP[], - int *label, int *label_old, double *label_factor, int ioflag) + doublereal solveSP:: + calc_t(doublereal netProdRateSolnSP[], doublereal XMolSolnSP[], + int *label, int *label_old, doublereal *label_factor, int ioflag) { int k, isp, nsp, kstart; - double inv_timeScale = 1.0E-10; - double sden, tmp; + doublereal inv_timeScale = 1.0E-10; + doublereal sden, tmp; int kindexSP = 0; *label = 0; int ispSpecial = 0; @@ -1025,8 +1025,8 @@ namespace Cantera { */ #ifdef DEBUG_SOLVESP void solveSP::printResJac(int ioflag, int neq, const Array2D &Jac, - double resid[], double wtRes[], - double norm) + doublereal resid[], doublereal wtRes[], + doublereal norm) { int i, j, isp, nsp, irowKSI, irowISP; int kstartKSI; @@ -1085,11 +1085,11 @@ namespace Cantera { /* * Optional printing at the start of the solveSP problem */ - void solveSP::print_header(int ioflag, int ifunc, double time_scale, - int damping, double reltol, double abstol, - double TKelvin, - double PGas, double netProdRate[], - double XMolKinSpecies[]) { + void solveSP::print_header(int ioflag, int ifunc, doublereal time_scale, + int damping, doublereal reltol, doublereal abstol, + doublereal TKelvin, + doublereal PGas, doublereal netProdRate[], + doublereal XMolKinSpecies[]) { if (ioflag) { printf("\n================================ SOLVESP CALL SETUP " "========================================\n"); @@ -1194,13 +1194,13 @@ namespace Cantera { } } - void solveSP::printIteration(int ioflag, double damp, int label_d, + void solveSP::printIteration(int ioflag, doublereal damp, int label_d, int label_t, - double inv_t, double t_real, int iter, - double update_norm, double resid_norm, - double netProdRate[], double CSolnSP[], - double resid[], double XMolSolnSP[], - double wtSpecies[], int dim, bool do_time) + doublereal inv_t, doublereal t_real, int iter, + doublereal update_norm, doublereal resid_norm, + doublereal netProdRate[], doublereal CSolnSP[], + doublereal resid[], doublereal XMolSolnSP[], + doublereal wtSpecies[], int dim, bool do_time) { int i, k; string nm; @@ -1278,14 +1278,14 @@ namespace Cantera { } /* printIteration */ - void solveSP::printFinal(int ioflag, double damp, int label_d, int label_t, - double inv_t, double t_real, int iter, - double update_norm, double resid_norm, - double netProdRateKinSpecies[], const double CSolnSP[], - const double resid[], double XMolSolnSP[], - const double wtSpecies[], const double wtRes[], + void solveSP::printFinal(int ioflag, doublereal damp, int label_d, int label_t, + doublereal inv_t, doublereal t_real, int iter, + doublereal update_norm, doublereal resid_norm, + doublereal netProdRateKinSpecies[], const doublereal CSolnSP[], + const doublereal resid[], doublereal XMolSolnSP[], + const doublereal wtSpecies[], const doublereal wtRes[], int dim, bool do_time, - double TKelvin, double PGas) + doublereal TKelvin, doublereal PGas) { int i, k; string nm; @@ -1363,7 +1363,7 @@ namespace Cantera { } printf("---------------------------------------------------------------" "---------------------------------------------\n"); - double *XMolKinSpecies = DATA_PTR(m_numEqn2); + doublereal *XMolKinSpecies = DATA_PTR(m_numEqn2); kindexSP = 0; for (int isp = 0; isp < m_numSurfPhases; isp++) { InterfaceKinetics *m_kin = m_objects[isp]; @@ -1417,7 +1417,7 @@ namespace Cantera { #ifdef DEBUG_SOLVESP void solveSP:: - printIterationHeader(int ioflag, double damp,double inv_t, double t_real, + printIterationHeader(int ioflag, doublereal damp,doublereal inv_t, doublereal t_real, int iter, bool do_time) { if (ioflag > 1) { diff --git a/Cantera/src/kinetics/solveSP.h b/Cantera/src/kinetics/solveSP.h index f4d679d3e..d47113175 100644 --- a/Cantera/src/kinetics/solveSP.h +++ b/Cantera/src/kinetics/solveSP.h @@ -249,45 +249,45 @@ namespace Cantera { * Note the actual converged solution is returned as part of the * internal state of the InterfaceKinetics objects. */ - int solveSurfProb(int ifunc, double time_scale, double TKelvin, - double PGas, double reltol, double abstol); + int solveSurfProb(int ifunc, doublereal time_scale, doublereal TKelvin, + doublereal PGas, doublereal reltol, doublereal abstol); private: //! Printing routine that gets called at the start of every //! invocation - void print_header(int ioflag, int ifunc, double time_scale, - int damping, double reltol, double abstol, - double TKelvin, double PGas, double netProdRate[], - double XMolKinSpecies[]); + void print_header(int ioflag, int ifunc, doublereal time_scale, + int damping, doublereal reltol, doublereal abstol, + doublereal TKelvin, doublereal PGas, doublereal netProdRate[], + doublereal XMolKinSpecies[]); #ifdef DEBUG_SOLVESP void printResJac(int ioflag, int neq, const Array2D &Jac, - double resid[], double wtResid[], double norm); + doublereal resid[], doublereal wtResid[], doublereal norm); #endif //! Printing routine that gets called after every iteration - void printIteration(int ioflag, double damp, int label_d, int label_t, - double inv_t, double t_real, int iter, - double update_norm, double resid_norm, - double netProdRate[], double CSolnSP[], - double resid[], double XMolSolnSP[], - double wtSpecies[], int dim, bool do_time); + void printIteration(int ioflag, doublereal damp, int label_d, int label_t, + doublereal inv_t, doublereal t_real, int iter, + doublereal update_norm, doublereal resid_norm, + doublereal netProdRate[], doublereal CSolnSP[], + doublereal resid[], doublereal XMolSolnSP[], + doublereal wtSpecies[], int dim, bool do_time); //! Print a summary of the solution /*! * */ - void printFinal(int ioflag, double damp, int label_d, int label_t, - double inv_t, double t_real, int iter, - double update_norm, double resid_norm, - double netProdRateKinSpecies[], const double CSolnSP[], - const double resid[], double XMolSolnSP[], - const double wtSpecies[], const double wtRes[], + void printFinal(int ioflag, doublereal damp, int label_d, int label_t, + doublereal inv_t, doublereal t_real, int iter, + doublereal update_norm, doublereal resid_norm, + doublereal netProdRateKinSpecies[], const doublereal CSolnSP[], + const doublereal resid[], doublereal XMolSolnSP[], + const doublereal wtSpecies[], const doublereal wtRes[], int dim, bool do_time, - double TKelvin, double PGas); + doublereal TKelvin, doublereal PGas); //! Calculate a conservative delta T to use in a pseudo-steady state //! algorithm @@ -320,9 +320,9 @@ namespace Cantera { * * @return Returns the 1. / delta T to be used on the next step */ - double calc_t(double netProdRateSolnSP[], double XMolSolnSP[], + doublereal calc_t(doublereal netProdRateSolnSP[], doublereal XMolSolnSP[], int *label, int *label_old, - double *label_factor, int ioflag); + doublereal *label_factor, int ioflag); //! Calculate the solution and residual weights /*! @@ -335,9 +335,9 @@ namespace Cantera { * @param abstol Absolute error tolerance * @param reltol Relative error tolerance */ - void calcWeights(double wtSpecies[], double wtResid[], - const Array2D &Jac, const double CSolnSP[], - const double abstol, const double reltol); + void calcWeights(doublereal wtSpecies[], doublereal wtResid[], + const Array2D &Jac, const doublereal CSolnSP[], + const doublereal abstol, const doublereal reltol); #ifdef DEBUG_SOLVESP //! Utility routine to print a header for high lvls of debugging @@ -350,22 +350,22 @@ namespace Cantera { * @param do_time boolean indicating whether time stepping is taking * place */ - void printIterationHeader(int ioflag, double damp, - double inv_t, double t_real, int iter, + void printIterationHeader(int ioflag, doublereal damp, + doublereal inv_t, doublereal t_real, int iter, bool do_time); #endif /** * Update the surface states of the surface phases. */ - void updateState(const double* cSurfSpec); + void updateState(const doublereal *cSurfSpec); //! Update mole fraction vector consisting of unknowns in surface problem /*! * @param XMolSolnSP Vector of mole fractions for the unknowns in the * surface problem. */ - void updateMFSolnSP(double *XMolSolnSP); + void updateMFSolnSP(doublereal * XMolSolnSP); //! Update the mole fraction vector for a specific kinetic species vector //! corresponding to one InterfaceKinetics object @@ -376,7 +376,7 @@ namespace Cantera { * phases in the InterfaceKinetics object * @param isp ID of the InterfaceKinetics Object. */ - void updateMFKinSpecies(double *XMolKinSp, int isp); + void updateMFKinSpecies(doublereal *XMolKinSp, int isp); //! Update the vector that keeps track of the largest species in each @@ -385,7 +385,7 @@ namespace Cantera { * @param CsolnSP Vector of the current values of the surface concentrations * in all of the surface species. */ - void evalSurfLarge(const double *CSolnSP); + void evalSurfLarge(const doublereal *CSolnSP); //! Main Function evalulation /*! @@ -398,8 +398,8 @@ namespace Cantera { * @param do_time Calculate a time dependent residual * @param deltaT Delta time for time dependent problem. */ - void fun_eval(double* resid, const double *CSolnSP, - const double *CSolnOldSP, const bool do_time, const double deltaT); + void fun_eval(doublereal* resid, const doublereal *CSolnSP, + const doublereal *CSolnOldSP, const bool do_time, const doublereal deltaT); //! Main routine that calculates the current residual and Jacobian /*! @@ -414,10 +414,10 @@ namespace Cantera { * @param do_time Calculate a time dependent residual * @param deltaT Delta time for time dependent problem. */ - void resjac_eval(std::vector& JacCol, double* resid, - double *CSolnSP, - const double *CSolnSPOld, const bool do_time, - const double deltaT); + void resjac_eval(std::vector& JacCol, doublereal * resid, + doublereal *CSolnSP, + const doublereal *CSolnSPOld, const bool do_time, + const doublereal deltaT); //! Pointer to the manager of the implicit surface chemistry //! problem @@ -581,10 +581,10 @@ namespace Cantera { /*! * units are (kmol/m2) */ - double m_atol; + doublereal m_atol; //! m_rtol is the relative error tolerance. - double m_rtol; + doublereal m_rtol; //! maximum value of the time step /*! @@ -669,7 +669,7 @@ namespace Cantera { * The "dim" by "dim" computed Jacobian matrix for the * local Newton's method. */ - std::vector m_JacCol; + std::vector m_JacCol; //! Jacobian /*! From 3587de40b748e2c0068eba7f543fa75c6485eee7 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 15 Jan 2010 20:22:09 +0000 Subject: [PATCH 6/7] Doxygen update on SingleSpeciesTP double to doublereal conversions made sure const parameters match on setTemperature() --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 4 +- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 2 +- Cantera/src/thermo/SingleSpeciesTP.cpp | 108 +++++++++++++----- Cantera/src/thermo/SingleSpeciesTP.h | 114 ++++++++++--------- Cantera/src/thermo/VPStandardStateTP.cpp | 4 +- Cantera/src/thermo/VPStandardStateTP.h | 6 +- Cantera/src/thermo/WaterProps.h | 22 ++-- 7 files changed, 156 insertions(+), 104 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index aaa88fe7c..df90bac16 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -615,9 +615,9 @@ namespace Cantera { // This is temporary. We will get rid of this - void IonsFromNeutralVPSSTP::setTemperature(doublereal t) { + void IonsFromNeutralVPSSTP::setTemperature(const doublereal temp) { double p = pressure(); - IonsFromNeutralVPSSTP::setState_TP(t, p); + IonsFromNeutralVPSSTP::setState_TP(temp, p); } // This is temporary. We will get rid of this diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index f9070fa0c..88b05e786 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -458,7 +458,7 @@ namespace Cantera { * @{ */ - virtual void setTemperature(doublereal t); + virtual void setTemperature(const doublereal t); virtual void setPressure(doublereal p); //! Set the temperature (K) and pressure (Pa) diff --git a/Cantera/src/thermo/SingleSpeciesTP.cpp b/Cantera/src/thermo/SingleSpeciesTP.cpp index 3bdfe52b3..8e8372c47 100644 --- a/Cantera/src/thermo/SingleSpeciesTP.cpp +++ b/Cantera/src/thermo/SingleSpeciesTP.cpp @@ -232,20 +232,29 @@ namespace Cantera { * of the zeroeth species. */ - /** - * Get the array of chemical potentials at unit activity - * These are the standard state chemical potentials. - * \f$ \mu^0_k \f$. + + // Get the array of chemical potentials at unit activity + /* + * These are the standard state chemical potentials. \f$ \mu^0_k \f$. + * + * @param mu On return, Contains the chemical potential of the single species + * and the phase. Units are J / kmol . Length = 1 */ void SingleSpeciesTP::getChemPotentials(doublereal* mu) const { getStandardChemPotentials(mu); } - /** - * Get the array of non-dimensional species chemical potentials - * These are partial molar Gibbs free energies. - * \f$ \mu_k / \hat R T \f$. + + // Get the array of non-dimensional species chemical potentials + // These are partial molar Gibbs free energies. + /* + * These are the standard state dimensionless chemical potentials. + * \f$ \mu_k / \hat R T \f$. + * * Units: unitless + * + * @param murt On return, Contains the chemical potential / RT of the single species + * and the phase. Units are unitless. Length = 1 */ void SingleSpeciesTP::getChemPotentials_RT(doublereal* murt) const { getStandardChemPotentials(murt); @@ -253,21 +262,27 @@ namespace Cantera { murt[0] /= rt; } - /** - * Get the species electrochemical potentials. Units: J/kmol. + // Get the species electrochemical potentials. Units: J/kmol. + /* * This method adds a term \f$ Fz_k \phi_k \f$ to * each chemical potential. * - * This is resolved here. A single single species phase - * is not allowed to have anything other than a zero - * charge. + * This is resolved here. A single species phase + * is not allowed to have anything other than a zero charge. + * + * @param murt On return, Contains the chemical potential / RT of the single species + * and the phase. Units are unitless. Length = 1 */ void SingleSpeciesTP::getElectrochemPotentials(doublereal* mu) const { getChemPotentials(mu); } - /** - * Get the species partial molar enthalpies. Units: J/kmol. + // Get the species partial molar enthalpies. Units: J/kmol. + /* + * These are the phase enthalpies. \f$ h_k \f$. + * + * @param hbar On return, Contains the enthalpy of the single species + * and the phase. Units are J / kmol . Length = 1 */ void SingleSpeciesTP:: getPartialMolarEnthalpies(doublereal* hbar) const { @@ -276,8 +291,15 @@ namespace Cantera { hbar[0] *= _rt; } - /** - * Get the species partial molar internal energies. Units: J/kmol. + // Get the species partial molar internal energies. Units: J/kmol. + /* + * These are the phase internal energies. \f$ u_k \f$. + * + * This member function is resolved here. A single species phase obtains its + * thermo from the standard state function. + * + * @param ubar On return, Contains the internal energy of the single species + * and the phase. Units are J / kmol . Length = 1 */ void SingleSpeciesTP:: getPartialMolarIntEnergies(doublereal* ubar) const { @@ -286,8 +308,15 @@ namespace Cantera { ubar[0] *= _rt; } - /** - * Get the species partial molar entropy. Units: J/kmol K. + // Get the species partial molar entropy. Units: J/kmol K. + /* + * This is the phase entropy. \f$ s(T,P) = s_o(T,P) \f$. + * + * This member function is resolved here. A single species phase obtains its + * thermo from the standard state function. + * + * @param sbar On return, Contains the entropy of the single species + * and the phase. Units are J / kmol / K . Length = 1 */ void SingleSpeciesTP:: getPartialMolarEntropies(doublereal* sbar) const { @@ -295,16 +324,30 @@ namespace Cantera { sbar[0] *= GasConstant; } - /** - * Get the species partial molar Heat Capacities. Units: J/kmol K. + // Get the species partial molar Heat Capacities. Units: J/ kmol K. + /* + * This is the phase heat capacity. \f$ Cp(T,P) = Cp_o(T,P) \f$. + * + * This member function is resolved here. A single species phase obtains its + * thermo from the standard state function. + * + * @param cpbar On return, Contains the heat capacity of the single species + * and the phase. Units are J / kmol / K . Length = 1 */ void SingleSpeciesTP::getPartialMolarCp(doublereal* cpbar) const { getCp_R(cpbar); cpbar[0] *= GasConstant; } - - /** - * Get the species partial molar volumes. Units: m^3/kmol. + + // Get the species partial molar volumes. Units: m^3/kmol. + /* + * This is the phase molar volume. \f$ V(T,P) = V_o(T,P) \f$. + * + * This member function is resolved here. A single species phase obtains its + * thermo from the standard state function. + * + * @param cpbar On return, Contains the molar volume of the single species + * and the phase. Units are m^3 / kmol. Length = 1 */ void SingleSpeciesTP::getPartialMolarVolumes(doublereal* vbar) const { double mw = molecularWeight(0); @@ -317,7 +360,7 @@ namespace Cantera { * ----- */ - /** + /* * Get the dimensional Gibbs functions for the standard * state of the species at the current T and P. */ @@ -326,14 +369,17 @@ namespace Cantera { gpure[0] *= GasConstant * temperature(); } - /** - * Get the molar volumes of each species in their standard - * states at the current - * T and P of the solution. - * units = m^3 / kmol + + // Get the molar volumes of each species in their standard + // states at the current T and P of the solution. + /* + * units = m^3 / kmol * * We resolve this function at this level, by assigning - * the molec weight divided by the phase density + * the molecular weight divided by the phase density + * + * @param vbar On output this contains the standard volume of the species + * and phase (m^3/kmol). Vector of length 1 */ void SingleSpeciesTP::getStandardVolumes(doublereal* vbar) const { double mw = molecularWeight(0); diff --git a/Cantera/src/thermo/SingleSpeciesTP.h b/Cantera/src/thermo/SingleSpeciesTP.h index 59e726bf2..8375b1eae 100644 --- a/Cantera/src/thermo/SingleSpeciesTP.h +++ b/Cantera/src/thermo/SingleSpeciesTP.h @@ -256,49 +256,47 @@ namespace Cantera { * standard state functions for species 0 */ - /** - * Get the array of non-dimensional species chemical potentials - * These are partial molar Gibbs free energies. - * \f$ \mu_k / \hat R T \f$. + //! Get the array of non-dimensional species chemical potentials + //! These are partial molar Gibbs free energies. + /*! + * These are the phase, partial molar, and the standard state + * dimensionless chemical potentials. + * \f$ \mu_k / \hat R T \f$. + * * Units: unitless * - * This function is resolved here by calling the standard state - * thermo function. - * - * @param mu Output vector of dimensionless chemical potentials. - * Length: m_kk. + * @param murt On return, Contains the chemical potential / RT of the single species + * and the phase. Units are unitless. Length = 1 */ - void getChemPotentials_RT(doublereal* mu) const; + void getChemPotentials_RT(doublereal* murt) const; - /** - * Get the species chemical potentials in the solution - * These are partial molar Gibbs free energies. - * Units: J/kmol. + //! Get the array of chemical potentials + /*! + * These are the phase, partial molar, and the standard state chemical potentials. + * \f$ \mu(T,P) = \mu^0_k(T,P) \f$. * - * This function is resolved here by calling the standard state - * thermo function. - * - * @param mu Output vector of species chemical - * potentials. Length: m_kk. Units: J/kmol + * @param mu On return, Contains the chemical potential of the single species + * and the phase. Units are J / kmol . Length = 1 */ void getChemPotentials(doublereal* mu) const; - /** - * Get the species electrochemical potentials. Units: J/kmol. + //! Get the species electrochemical potentials. Units: J/kmol. + /*! * This method adds a term \f$ Fz_k \phi_k \f$ to * each chemical potential. * - * This is resolved here. A single single species phase - * is not allowed to have anything other than a zero - * charge. + * This is resolved here. A single species phase + * is not allowed to have anything other than a zero charge. * - * @param mu Output vector of species electrochemical - * potentials. Length: m_kk. Units: J/kmol + * @param mu On return, Contains the electrochemical potential of the single species + * and the phase. Units J/kmol . Length = 1 */ void getElectrochemPotentials(doublereal* mu) const; //! Get the species partial molar enthalpies. Units: J/kmol. /*! + * These are the phase enthalpies. \f$ h_k \f$. + * * This function is resolved here by calling the standard state * thermo function. * @@ -307,43 +305,52 @@ namespace Cantera { */ void getPartialMolarEnthalpies(doublereal* hbar) const; - //! Get the species partial molar enthalpies. Units: J/kmol. + + //! Get the species partial molar internal energies. Units: J/kmol. /*! - * This function is resolved here by calling the standard state - * thermo function. + * These are the phase internal energies. \f$ u_k \f$. * - * @param ubar Output vector of speciar partial molar internal energies. - * Length = m_kk. units are J/kmol. + * This member function is resolved here. A single species phase obtains its + * thermo from the standard state function. + * + * @param ubar On return, Contains the internal energy of the single species + * and the phase. Units are J / kmol . Length = 1 */ virtual void getPartialMolarIntEnergies(doublereal* ubar) const; - //! Get the species partial molar entropies. Units: J/kmol/K. + //! Get the species partial molar entropy. Units: J/kmol K. /*! - * This function is resolved here by calling the standard state - * thermo function. + * This is the phase entropy. \f$ s(T,P) = s_o(T,P) \f$. * - * @param sbar Output vector of species partial molar entropies. - * Length = 1. units are J/kmol/K. + * This member function is resolved here. A single species phase obtains its + * thermo from the standard state function. + * + * @param sbar On return, Contains the entropy of the single species + * and the phase. Units are J / kmol / K . Length = 1 */ void getPartialMolarEntropies(doublereal* sbar) const; - //! Get the species partial molar heat capacties. Units: J/kmol/K. + //! Get the species partial molar Heat Capacities. Units: J/ kmol /K. /*! - * This function is resolved here by calling the standard state - * thermo function. + * This is the phase heat capacity. \f$ Cp(T,P) = Cp_o(T,P) \f$. * - * @param cpbar Output vector of species partial molar heat capacities - * Length = 1. units are J/kmol/K. + * This member function is resolved here. A single species phase obtains its + * thermo from the standard state function. + * + * @param cpbar On return, Contains the heat capacity of the single species + * and the phase. Units are J / kmol / K . Length = 1 */ void getPartialMolarCp(doublereal* cpbar) const; - //! Get the species partial molar volumes. Units: m^3/kmol. /*! - * This function is resolved here by calling the density function. + * This is the phase molar volume. \f$ V(T,P) = V_o(T,P) \f$. * - * @param vbar Output vector of speciar partial molar volumes. - * Length = 1. units are m^3/kmol. + * This member function is resolved here. A single species phase obtains its + * thermo from the standard state function. + * + * @param vbar On return, Contains the molar volume of the single species + * and the phase. Units are m^3 / kmol. Length = 1 */ void getPartialMolarVolumes(doublereal* vbar) const; @@ -367,19 +374,18 @@ namespace Cantera { */ void getPureGibbs(doublereal* gpure) const; - /** - * Get the molar volumes of each species in their standard - * states at the current - * T and P of the solution. - * units = m^3 / kmol + //! Get the molar volumes of each species in their standard + //! states at the current T and P of the solution. + /*! + * units = m^3 / kmol * * We resolve this function at this level, by assigning - * the molec weight divided by the phase density + * the molecular weight divided by the phase density * - * @param vol vector of length one, containing the standard volume - * of the phase. + * @param vbar On output this contains the standard volume of the species + * and phase (m^3/kmol). Vector of length 1 */ - void getStandardVolumes(doublereal *vol) const; + void getStandardVolumes(doublereal *vbar) const; //@} diff --git a/Cantera/src/thermo/VPStandardStateTP.cpp b/Cantera/src/thermo/VPStandardStateTP.cpp index 2c1da45e1..0367dd46d 100644 --- a/Cantera/src/thermo/VPStandardStateTP.cpp +++ b/Cantera/src/thermo/VPStandardStateTP.cpp @@ -357,8 +357,8 @@ namespace Cantera { } - void VPStandardStateTP::setTemperature(doublereal t) { - setState_TP(t, m_Pcurrent); + void VPStandardStateTP::setTemperature(const doublereal temp) { + setState_TP(temp, m_Pcurrent); updateStandardStateThermo(); } diff --git a/Cantera/src/thermo/VPStandardStateTP.h b/Cantera/src/thermo/VPStandardStateTP.h index 4faed6a10..988ac937a 100644 --- a/Cantera/src/thermo/VPStandardStateTP.h +++ b/Cantera/src/thermo/VPStandardStateTP.h @@ -282,9 +282,9 @@ namespace Cantera { * make sense to calculate the standard state without first * setting T and P. * - * @param T Temperature (kelvin) + * @param temp Temperature (kelvin) */ - virtual void setTemperature(const doublereal T); + virtual void setTemperature(const doublereal temp); //! Set the internally storred pressure (Pa) at constant @@ -296,7 +296,7 @@ namespace Cantera { * * @param p input Pressure (Pa) */ - virtual void setPressure(const doublereal p); + virtual void setPressure(doublereal p); protected: /** diff --git a/Cantera/src/thermo/WaterProps.h b/Cantera/src/thermo/WaterProps.h index b6099f7df..a738e20de 100644 --- a/Cantera/src/thermo/WaterProps.h +++ b/Cantera/src/thermo/WaterProps.h @@ -164,7 +164,7 @@ namespace Cantera { * * units = returns density in kg m-3. */ - static double density_T(double T, double P, int ifunc); + static doublereal density_T(doublereal T, doublereal P, int ifunc); //! Bradley-Pitzer equation for the dielectric constant @@ -200,7 +200,7 @@ namespace Cantera { * value at 25C and 1 atm, relEps = 78.38 * */ - double relEpsilon(double T, double P_pascal, int ifunc = 0); + doublereal relEpsilon(doublereal T, doublereal P_pascal, int ifunc = 0); //! ADebye calculates the value of A_Debye as a function @@ -243,7 +243,7 @@ namespace Cantera { * - ifunc = 3 return pressure first derivative * . * - * @return Returns a single double whose meaning depends on ifunc: + * @return Returns a single doublereal whose meaning depends on ifunc: * - ifunc = 0 return value * - ifunc = 1 return temperature derivative * - ifunc = 2 return temperature second derivative @@ -258,7 +258,7 @@ namespace Cantera { * the Pitzer table p. 99 to 4 significant digits at 25C. * and 20C. (Aphi = ADebye/3) */ - double ADebye(double T, double P, int ifunc); + doublereal ADebye(doublereal T, doublereal P, int ifunc); //! Returns the saturation pressure given the temperature @@ -266,7 +266,7 @@ namespace Cantera { * @param T temperature (kelvin) * @return returns the saturation pressure (pascal) */ - double satPressure(double T); + doublereal satPressure(doublereal T); //! Returns the density of water @@ -277,14 +277,14 @@ namespace Cantera { * @param T Temperature (kelvin) * @param P pressure (pascal) */ - double density_IAPWS(double T, double P); + doublereal density_IAPWS(doublereal T, doublereal P); //! Returns the density of water /*! * This function uses the internal state of the * underlying water object */ - double density_IAPWS() const; + doublereal density_IAPWS() const; //! returns the coefficient of thermal expansion @@ -292,14 +292,14 @@ namespace Cantera { * @param T Temperature (kelvin) * @param P pressure (pascal) */ - double coeffThermalExp_IAPWS(double T, double P); + doublereal coeffThermalExp_IAPWS(doublereal T, doublereal P); //! Returns the isothermal compressibility of water /*! * @param T temperature in kelvin * @param P pressure in pascal */ - double isothermalCompressibility_IAPWS(double T, double P); + doublereal isothermalCompressibility_IAPWS(doublereal T, doublereal P); //! Returns the viscosity of water at the current conditions //! (kg/m/s) @@ -316,7 +316,7 @@ namespace Cantera { * for steam and for water, even near the critical point. * Pressures above 500 MPa and temperature above 900 C are suspect. */ - double viscosityWater() const; + doublereal viscosityWater() const; //! Returns the thermal conductivity of water at the current conditions //! (W/m/K) @@ -333,7 +333,7 @@ namespace Cantera { * for steam and for water, even near the critical point. * Pressures above 500 MPa and temperature above 900 C are suspect. */ - double thermalConductivityWater() const; + doublereal thermalConductivityWater() const; From a9e35724c2a19ec84d32e3c0996a712f8b74096a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 15 Jan 2010 20:26:59 +0000 Subject: [PATCH 7/7] Upgraded doxygen configuration file. --- tools/doc/Cantera.cfg.in | 1616 +++++++++++++++++++++++++++++++++++--- 1 file changed, 1510 insertions(+), 106 deletions(-) diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index d0a8ea9f9..0ca8c8c93 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -1,16 +1,91 @@ -# Doxyfile 1.4.2 +# Doxyfile 1.6.2 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + PROJECT_NAME = Cantera + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + PROJECT_NUMBER = 1.7 + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + OUTPUT_DIRECTORY = @ctroot@/tools/doc + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + OUTPUT_LANGUAGE = English -USE_WINDOWS_ENCODING = NO + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + ABBREVIATE_BRIEF = "The $name class" \ "The $name widget" \ "The $name file" \ @@ -22,148 +97,691 @@ ABBREVIATE_BRIEF = "The $name class" \ a \ an \ the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + ALWAYS_DETAILED_SEC = YES + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + INLINE_INHERITED_MEMB = YES + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + FULL_PATH_NAMES = NO -STRIP_FROM_PATH = -STRIP_FROM_INC_PATH = + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + JAVADOC_AUTOBRIEF = YES + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + MULTILINE_CPP_IS_BRIEF = NO -DETAILS_AT_TOP = YES + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + INHERIT_DOCS = YES -DISTRIBUTE_GROUP_DOC = NO + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + TAB_SIZE = 8 -ALIASES = + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). 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If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + HIDE_IN_BODY_DOCS = YES + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + INTERNAL_DOCS = YES + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + HIDE_SCOPE_NAMES = YES + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + SHOW_INCLUDE_FILES = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + GENERATE_DEPRECATEDLIST= YES -ENABLED_SECTIONS = + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + SHOW_DIRECTORIES = YES -FILE_VERSION_FILTER = + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + WARN_NO_PARAMDOC = YES + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + WARN_FORMAT = "$file:$line: $text" -WARN_LOGFILE = + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- -INPUT = ../../Cantera/src \ - ../../Cantera/src/base \ - ../../Cantera/src/numerics \ + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = ../../Cantera/src \ + ../../Cantera/src/base \ + ../../Cantera/src/numerics \ ../../Cantera/src/thermo \ ../../Cantera/src/equil \ ../../Cantera/src/kinetics \ ../../Cantera/src/transport \ ../../Cantera/cxx/include \ doxyinput -FILE_PATTERNS = Kinetics.h Kinetics.cpp \ - FactoryBase.h misc.cpp \ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = Kinetics.h \ + Kinetics.cpp \ + FactoryBase.h \ + misc.cpp \ ct_defs.h \ logger.h \ global.h \ units.h \ ctexceptions.h \ *.txt \ - xml.h xml.cpp \ - ctml.h ctml.cpp ct2ctml.cpp \ - stringUtils.h stringUtils.cpp \ - plots.h plots.cpp \ - PrintCtrl.h PrintCtrl.cpp \ - LogPrintCtrl.h LogPrintCtrl.cpp \ - clockWC.h clockWC.cpp \ - Array.h vec_functions.h \ + xml.h \ + xml.cpp \ + ctml.h \ + ctml.cpp \ + ct2ctml.cpp \ + stringUtils.h \ + stringUtils.cpp \ + plots.h \ + plots.cpp \ + PrintCtrl.h \ + PrintCtrl.cpp \ + LogPrintCtrl.h \ + LogPrintCtrl.cpp \ + clockWC.h \ + clockWC.cpp \ + Array.h \ + vec_functions.h \ equilibrium.h \ - ThermoPhase.h ThermoPhase.cpp \ - Phase.h Phase.cpp \ - State.h State.cpp \ - Constituents.h Constituents.cpp \ - Elements.h Elements.cpp \ - importCTML.cpp importCTML.h \ - ThermoFactory.h ThermoFactory.cpp \ - IdealGasPhase.h IdealGasPhase.cpp \ - SurfPhase.h EdgePhase.h SurfPhase.cpp \ - LatticePhase.h LatticePhase.cpp \ - SpeciesThermoFactory.h SpeciesThermoFactory.cpp \ - speciesThermoTypes.h SpeciesThermoMgr.h SpeciesThermoInterpType.h \ - PDSS.h PDSS.cpp \ + ThermoPhase.h \ + ThermoPhase.cpp \ + Phase.h \ + Phase.cpp \ + State.h \ + State.cpp \ + Constituents.h \ + Constituents.cpp \ + Elements.h \ + Elements.cpp \ + importCTML.cpp \ + importCTML.h \ + ThermoFactory.h \ + ThermoFactory.cpp \ + IdealGasPhase.h \ + IdealGasPhase.cpp \ + SurfPhase.h \ + EdgePhase.h \ + SurfPhase.cpp \ + LatticePhase.h \ + LatticePhase.cpp \ + SpeciesThermoFactory.h \ + SpeciesThermoFactory.cpp \ + speciesThermoTypes.h \ + SpeciesThermoMgr.h \ + SpeciesThermoInterpType.h \ + PDSS.h \ + PDSS.cpp \ SpeciesThermo.h \ - NasaThermo.h NasaPoly1.h NasaPoly2.h \ - ShomateThermo.h ShomatePoly.h SimpleThermo.h \ - GeneralSpeciesThermo.h GeneralSpeciesThermo.cpp \ - ConstCpPoly.h ConstCpPoly.cpp Mu0Poly.h Mu0Poly.cpp \ - utilities.h phasereport.cpp \ - VPStandardStateTP.h VPStandardStateTP.cpp \ - SingleSpeciesTP.h SingleSpeciesTP.cpp \ - MetalSHEelectrons.h MetalSHEelectrons.cpp \ - MolalityVPSSTP.h MolalityVPSSTP.cpp \ - IdealMolalSoln.h IdealMolalSoln.cpp \ - IdealSolidSolnPhase.h IdealSolidSolnPhase.cpp \ - StoichSubstanceSSTP.h StoichSubstanceSSTP.cpp \ - DebyeHuckel.h DebyeHuckel.cpp \ - MineralEQ3.h MineralEQ3.cpp \ - HMWSoln.h HMWSoln.cpp HMWSoln_input.cpp \ - VPSSMgr.h VPSSMgr.cpp VPSSMgr_types.h \ - VPSSMgr_ConstVol.h VPSSMgr_ConstVol.cpp \ - VPSSMgr_IdealGas.h VPSSMgr_IdealGas.cpp \ - VPSSMgr_Water_ConstVol.h VPSSMgr_Water_ConstVol.cpp \ - VPSSMgr_Water_HKFT.h VPSSMgr_Water_HKFT.cpp \ - VPSSMgr_General.h VPSSMgr_General.cpp \ - VPSSMgrFactory.h VPSSMgrFactory.cpp \ - PDSS_ConstVol.h PDSS_ConstVol.cpp \ - PDSS_IdealGas.h PDSS_IdealGas.cpp \ - PDSS_Water.h PDSS_Water.cpp \ - PDSS_HKFT.h PDSS_HKFT.cpp \ - PDSS_SSVol.h PDSS_SSVol.cpp \ - IdealSolnGasVPSS.h IdealSolnGasVPSS.cpp \ - ConstDensityThermo.h ConstDensityThermo.cpp \ - WaterPropsIAPWSphi.h WaterPropsIAPWSphi.cpp \ - WaterPropsIAPWS.h WaterPropsIAPWS.cpp \ - WaterSSTP.h WaterSSTP.cpp \ - WaterProps.h WaterProps.cpp \ - PureFluidPhase.h PureFluidPhase.cpp \ - equil.h MultiPhase.h MultiPhase.cpp BasisOptimize.cpp \ - Nasa9Poly1.h Nasa9Poly1.cpp \ - Nasa9PolyMultiTempRegion.h Nasa9PolyMultiTempRegion.cpp \ - vcs_internal.h vcs_defs.h \ - vcs_MultiPhaseEquil.h vcs_MultiPhaseEquil.cpp \ - FalloffFactory.h FalloffFactory.cpp + NasaThermo.h \ + NasaPoly1.h \ + NasaPoly2.h \ + ShomateThermo.h \ + ShomatePoly.h \ + SimpleThermo.h \ + GeneralSpeciesThermo.h \ + GeneralSpeciesThermo.cpp \ + ConstCpPoly.h \ + ConstCpPoly.cpp \ + Mu0Poly.h \ + Mu0Poly.cpp \ + utilities.h \ + phasereport.cpp \ + VPStandardStateTP.h \ + VPStandardStateTP.cpp \ + SingleSpeciesTP.h \ + SingleSpeciesTP.cpp \ + MetalSHEelectrons.h \ + MetalSHEelectrons.cpp \ + MolalityVPSSTP.h \ + MolalityVPSSTP.cpp \ + IdealMolalSoln.h \ + IdealMolalSoln.cpp \ + IdealSolidSolnPhase.h \ + IdealSolidSolnPhase.cpp \ + StoichSubstanceSSTP.h \ + StoichSubstanceSSTP.cpp \ + DebyeHuckel.h \ + DebyeHuckel.cpp \ + MineralEQ3.h \ + MineralEQ3.cpp \ + HMWSoln.h \ + HMWSoln.cpp \ + HMWSoln_input.cpp \ + VPSSMgr.h \ + VPSSMgr.cpp \ + VPSSMgr_types.h \ + VPSSMgr_ConstVol.h \ + VPSSMgr_ConstVol.cpp \ + VPSSMgr_IdealGas.h \ + VPSSMgr_IdealGas.cpp \ + VPSSMgr_Water_ConstVol.h \ + VPSSMgr_Water_ConstVol.cpp \ + VPSSMgr_Water_HKFT.h \ + VPSSMgr_Water_HKFT.cpp \ + VPSSMgr_General.h \ + VPSSMgr_General.cpp \ + VPSSMgrFactory.h \ + VPSSMgrFactory.cpp \ + PDSS_ConstVol.h \ + PDSS_ConstVol.cpp \ + PDSS_IdealGas.h \ + PDSS_IdealGas.cpp \ + PDSS_Water.h \ + PDSS_Water.cpp \ + PDSS_HKFT.h \ + PDSS_HKFT.cpp \ + PDSS_SSVol.h \ + PDSS_SSVol.cpp \ + IdealSolnGasVPSS.h \ + IdealSolnGasVPSS.cpp \ + ConstDensityThermo.h \ + ConstDensityThermo.cpp \ + WaterPropsIAPWSphi.h \ + WaterPropsIAPWSphi.cpp \ + WaterPropsIAPWS.h \ + WaterPropsIAPWS.cpp \ + WaterSSTP.h \ + WaterSSTP.cpp \ + WaterProps.h \ + WaterProps.cpp \ + PureFluidPhase.h \ + PureFluidPhase.cpp \ + equil.h \ + MultiPhase.h \ + MultiPhase.cpp \ + BasisOptimize.cpp \ + Nasa9Poly1.h \ + Nasa9Poly1.cpp \ + Nasa9PolyMultiTempRegion.h \ + Nasa9PolyMultiTempRegion.cpp \ + vcs_internal.h \ + vcs_defs.h \ + vcs_MultiPhaseEquil.h \ + vcs_MultiPhaseEquil.cpp \ + FalloffFactory.h \ + FalloffFactory.cpp + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + RECURSIVE = NO -EXCLUDE = CVS examples converters zeroD + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = CVS \ + examples \ + converters \ + zeroD + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + EXCLUDE_PATTERNS = *old/* \ *old_src/* \ *stl/* \ @@ -171,154 +789,940 @@ EXCLUDE_PATTERNS = *old/* \ *examples/* \ *test/* \ *tests/* + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + EXAMPLE_PATH = ../../examples \ ../../data/inputs \ ./doxyinput + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + EXAMPLE_PATTERNS = *.cpp \ *.h + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + EXAMPLE_RECURSIVE = NO -IMAGE_PATH = -INPUT_FILTER = -FILTER_PATTERNS = + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + FILTER_SOURCE_FILES = NO + #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + STRIP_CODE_COMMENTS = NO + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + VERBATIM_HEADERS = YES + #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + IGNORE_PREFIX = Cantera:: + #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + HTML_FILE_EXTENSION = .html -HTML_HEADER = -HTML_FOOTER = -HTML_STYLESHEET = + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = NO + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + GENERATE_HTMLHELP = YES -CHM_FILE = -HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + GENERATE_TREEVIEW = NO + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = NO + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be implemented using a PHP enabled web server instead of at the web client using Javascript. Doxygen will generate the search PHP script and index +# file to put on the web server. The advantage of the server based approach is that it scales better to large projects and allows full text search. The disadvances is that it is more difficult to setup +# and does not have live searching capabilities. + +SERVER_BASED_SEARCH = NO + #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + COMPACT_LATEX = YES + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + PAPER_TYPE = letter -EXTRA_PACKAGES = -LATEX_HEADER = + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + RTF_HYPERLINKS = NO -RTF_STYLESHEET_FILE = -RTF_EXTENSIONS_FILE = + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + MAN_LINKS = NO + #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + XML_OUTPUT = xml -XML_SCHEMA = -XML_DTD = + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + XML_PROGRAMLISTING = YES + #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + GENERATE_AUTOGEN_DEF = NO + #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + PERLMOD_PRETTY = YES -PERLMOD_MAKEVAR_PREFIX = + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + #--------------------------------------------------------------------------- -# Configuration options related to the preprocessor +# Configuration options related to the preprocessor #--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + MACRO_EXPANSION = YES + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + EXPAND_ONLY_PREDEF = YES + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + SEARCH_INCLUDES = YES -INCLUDE_PATH = -INCLUDE_FILE_PATTERNS = + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + PREDEFINED = WITH_HTML_LOGS \ WITH_PURE_FLUIDS \ THREAD_SAFE_CANTERA \ WITH_LATTICE_SOLID + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + EXPAND_AS_DEFINED = YES + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + SKIP_FUNCTION_MACROS = YES + #--------------------------------------------------------------------------- -# Configuration::additions related to external references +# Configuration::additions related to external references #--------------------------------------------------------------------------- -TAGFILES = -GENERATE_TAGFILE = + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + PERL_PATH = /usr/bin/perl + #--------------------------------------------------------------------------- -# Configuration options related to the dot tool +# Configuration options related to the dot tool #--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + HAVE_DOT = YES + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + TEMPLATE_RELATIONS = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + DOT_PATH = @GRAPHVIZDIR@ -DOTFILE_DIRS = -MAX_DOT_GRAPH_WIDTH = 1024 -MAX_DOT_GRAPH_HEIGHT = 1024 + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + DOT_CLEANUP = YES -#--------------------------------------------------------------------------- -# Configuration::additions related to the search engine -#--------------------------------------------------------------------------- -SEARCHENGINE = NO